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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtatttttcttaattttcaaattatagccaacataagaatttccttagagtggcttcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG

Basic information

species Glycine max
transcript GLYMA20G39250.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39250.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G43080.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttgtatttttcttaattttcaaattatagccaacataagaatttccttagagtggct-tcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG
        | |  ||||| ||  ||  |  | |   |   |   | |    |||  |||| | |  || | ||  | ||       |||  |  |||    ||   | |||||||||  | ||||||||||| |||||  |||| || |||||||||||| ||| |||  |  | |||||||||||||| |||||||| |||
------cttctccttcttcatcatcttagaacatttagtttggaagtacgtttattgtgggtgttcatcatatttcctcg------tttcttttcttatggttgctacacagTTCAATCTAAAGCGTGGTGGTCAGCGCGTAGCAACTATGCTTATGTATCTAACTGATGACGTCGAAGGAGGAGAAACTTATTTCCCTTTG

upper sequence: GLYMA20G39250.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttgtatttttcttaattttcaaattatagccaacataagaatttccttagagtggcttcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG
||||||| | |    ||   ||||  | | |          ||     || ||    | || |   ||||   | |   || |      ||||     ||||      ||||| ||||||||||||||||| || ||| |||| |||||||| || ||||||||||| ||| |||| || |||||||||||||||||  ||
gtaagttatttacccctgccttttttagtgacctttccttcaa-----tcttt----tagccttg-tgaa---ctagtaatga------gtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|151409088|gb|EV278896.1|EV278896
EST:     ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACT                         TTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
genomic: ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACTgtaagttgta ... tttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
EST: gi|151393423|gb|EV263298.1|EV263298
EST:     ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACT                         TTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
genomic: ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACTgtaagttgta ... tttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
EST: gi|151400878|gb|EV270692.1|EV270692
EST:     ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACT                         TTCA-CTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
genomic: ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACTgtaagttgta ... tttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
EST: gi|12496541|gb|BG047116.1|BG047116
EST:     ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACT                         TTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA
genomic: ACGAGAAGAATCAATATTACAAACCCCATCATGACTATTTTTCTGATACTgtaagttgta ... tttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggcttcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG
                     ctataac  putative branch site (score: 3)
                           ccttttgtgcctttct  CT-rich tract
                                      tttctttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtatttttcttaattttcaaattatagccaacataagaatttccttagagtggcttcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA